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Papers by Thomas Kuyper

Growth response of Pterocarpus soyauxii and Lophira alata seedlings to host soil mycorrhizal inoc... more Growth response of Pterocarpus soyauxii and Lophira alata seedlings to host soil mycorrhizal inocula in relation to land use types

Journal of Vegetation Science, 2016

Questions: Secondary succession in the tropics can follow alternative pathways. Land-use history ... more Questions: Secondary succession in the tropics can follow alternative pathways. Land-use history is known to engender alternative successional communities, but the underlying mechanisms driving and sustaining divergence remain unclear. In this study we aim to answer the following questions: (1) does previous land use act as a filter for species composition in secondary forests; and (2) what are the relative roles of management practices, soil properties and landscape composition in determining species composition? Location: Central Amazon, Brazil. Methods: We sampled trees, shrubs and palms (≥1cm diameter) in 38 early secondary forests (5 yr after abandonment) located along gradients of land-use intensity in five shifting cultivation landscapes. We measured the diameter and height of each sampled plant, identified it to species or morpho-species level and checked if it was resprouting or not. At each secondary forest we also collected soil samples for chemical and physical analyses and estimated the amount of old-growth forest surrounding it (landscape composition). Results: We found that previous land-use intensity determined species composition. With increasing land-use intensity, management practices of cut-andburn and associated reduction in soil quality filtered out seed-dependent species and favoured strong sprouters and species that can cope with low nutrient availability. Landscape composition had a weak effect on species assemblages. We found specific species assemblages and indicator species associated with different levels of previous land-use intensity. As a consequence of these local filters, species aand b-diversity decreased and therefore early successional communities became more similar to each other. Conclusion: Species composition of successional forests is strongly determined by different land-use intensities. Dispersal limitation has a limited effect on determining the composition of the dominant species. Filtering effects of management practices and soil quality determine the species dominating the canopy at early stages of succession and narrow down the range of species able to colonize and establish. This study highlights how land use shapes successional communities and suggests that alternative successional pathways are determined at early stages of succession. Therefore, accounting for land-use history is crucial to improve the understanding of tropical secondary succession. We present a list of indicator species for different levels of previous land-use intensity that can be used to support conservation and restoration decisions in the Amazon.

Arbuscular mycorrhizal symbiosis increases phosphorus uptake and productivity of mixtures of maize varieties compared to monocultures

Journal of Applied Ecology, 2020

Ecological intensification seeks to achieve crop yield increases by intensifying complementary or... more Ecological intensification seeks to achieve crop yield increases by intensifying complementary or facilitative interactions between plant species or varieties. Different species of arbuscular mycorrhizal fungi (AMF) exhibit niche differentiation and show selectivity towards certain plants, which can further enhance complementarity. It is not clear whether in the presence of one AMF species, where mycelial networks connect crop species, opportunities for complementarity effects may be reduced. We grew monocultures and mixtures of maize varieties in a greenhouse with one species of AMF, Funneliformis mosseae, during two consecutive years to investigate whether under such conditions the mycorrhizal symbiosis would affect complementarity and overyielding compared to non-mycorrhizal plants. Variety mixtures showed increased phosphatase activity and mycorrhizal colonization, enhanced phosphorus uptake and overyielding when plants were mycorrhizal. There was no overyielding when plants were non-mycorrhizal. The increase in relative yield total was due to complementarity effects. Synthesis and applications. Our study implies that appropriate agricultural management that enhances mycorrhizal fungal contribution to ecosystem services may result in overyielding in terms of yield or phosphorus uptake through mixing varieties within one crop species.

New Phytologist, 2021

Networks of friends and foes and the fate of tree seedlings Why are there so many different tree ... more Networks of friends and foes and the fate of tree seedlings Why are there so many different tree species in most tropical rainforests? Ecologists have increasingly turned to plant-soil feedback (PSF), the mutual interaction between plants and the soil biotic community, where plants modify, and are modified by, that soil biotic community. In the 1970s two ecologists, Daniel Janzen and Joseph Connell, independently proposed a mechanism to explain the persistence of species-rich communities through such feedbacks. The Janzen-Connell effect is based on conspecific negative density dependence (CNDD), implying larger juvenile mortality (seeds, seedlings, saplings) in the immediate vicinity of conspecific adult organisms. As a consequence of CNDD other species would be preferentially recruited under their canopy. Fungal pathogens are likely the major agent in causing seedling CNDD (Song & Corlett, 2021). Roots of tropical tree species are

ECY17-1266_SpringSapro10x10km_17jan2018

Spring saprotrophic fruiting fungi data: 10 x 10 km grid resolution of species fruiting days (ord... more Spring saprotrophic fruiting fungi data: 10 x 10 km grid resolution of species fruiting days (ordinal day; mean, 2.5 & 97.5 percentiles plus sample sizes) aggregated across 1970-2010. Associated bioclimatic meta-data for each grid are included as well. This dataset comprises saprotrophic fungal taxa fruiting in spring

Nitrogen availability mediates the priming effect of soil organic matter by preferentially altering the straw carbon-assimilating microbial community

Science of The Total Environment, 2022

Straw incorporation into soil increases carbon (C) sequestration but can induce priming effects (... more Straw incorporation into soil increases carbon (C) sequestration but can induce priming effects (PE), the enhanced breakdown of soil organic matter. The direction and magnitude of PE and the consequences for the C balance induced by straw addition depend on nitrogen (N) availability and soil management history. Using 13C-labeled maize straw, we conducted a 56-day incubation to determine the dynamics of PE and the underlying microbial mechanisms after straw and/or mineral N addition to three soils with contrasting cultivation and fertilization histories, i) unfertilized soil (Unfertilized), ii) 8 years farmyard manure amended soil (Manured), and iii) abandoned cropland soil (Abandoned). 13C-PLFAs (phospholipid fatty acids) were analyzed to identify microbial groups utilizing straw and to explore their contribution to the PE. Straw addition increased microbial biomass (MBC), activities of enzymes related to the C and N cycles, and changed microbial community composition. SOC decomposition was enhanced by microbes activated by straw addition, leading to a positive cumulative PE ranging from 494 to 789 μg C g-1 soil. The magnitude of positive PE and straw decomposition in the manured soil was higher than that in the unfertilized and abandoned soils due to larger MBC and higher enzyme activities, resulting in a lower net SOC gain. Compared with straw only, the combination of straw addition with N fertilizer did not influence MBC, but increased positive PE (average increase of 18.1%) and straw decomposition (17.1%), further limiting SOC gain. 13C-labeled fungi: bacteria ratios and Gram-positive (G+): negative (G-) bacteria ratios increased with the increasing PE after N fertilization, but soil-derived (un-labeled) PLFAs remained stable. Random forest analysis further showed that straw C-assimilating microbial attributes are important predictors in driving the greater PE after N addition. Our study highlights the importance of straw C-assimilating fungi and G+ bacteria in mediating N-induced PE in arable soils.

Conventional wisdom considers the mycorrhizal symbiosis as mutualistic because both the mycorrhiz... more Conventional wisdom considers the mycorrhizal symbiosis as mutualistic because both the mycorrhizal fungus and the mycorrhizal plant potentially benefit from the exchange of nutrients and carbon (C). Cases in which mycorrhizal plants are smaller than nonmycorrhizal plants have been reported (Klironomos, 2003). While these cases are often considered exceptions, they raise an important question of partner control. How do plant and fungal partners ensure that they are getting a ‘fair-deal’ for the resources they are trading, and avoid being cheated (Ghoul et al., 2014)? Does engaging in amutualistic partnership translate into consistent andmeasurable benefits? Recently, N€asholm et al. (2013) explicitly addressed the question of whether ectomycorrhizal fungi alleviate or aggravate nitrogen (N) limitation of conifers in boreal forests. They concluded that, in these systems, ectomycorrhizal fungi immobilize large quantities of N and thus drive N limitation for host plants. In this issue ...

During the last few years a large number of new mushroom genera have been described. In many case... more During the last few years a large number of new mushroom genera have been described. In many cases such new genera were proposed as a consequence of molecular phylogenetic research, whereas morphological support for these genera was in a number of cases not presented. In this paper we discuss a number of these changes (boletes, the previous genus Clitocybe; in both cases a large number of new genera were proposed). We also ask the question to what extent such changes have to be followed. At the end we introduce a number of criteria that are helpful in judging whether such new genera are indeed indicative of taxonomical progress. It is clear that many of the new genera do not (yet) fulfil these criteria

Recently the well-known genus Amanita has been split into two genera, Amanita, a genus of putativ... more Recently the well-known genus Amanita has been split into two genera, Amanita, a genus of putatively ectomycorrhizal fungi, and Saproamanita, a genus of putatively saprotrophic fungi. We disagree with this generic split and argue why Amanita should not be split. The proposal to split the genus does not conform to the recently proposed guidelines for publishing new genera. Concise amended characterizations are provided for the monophyletic family Amanitaceae and its two monophyletic genera Amanita and Limacella.2 The characterization of Amanita rests on a single, unique synapomorphy—schizohymenial ontogeny in its agaricoid and secotioid taxa. We propose a minimal reorganization of Amanita—removal of stirps Hesleri from subsection Vittadiniae. Some open issues in Amanita systematics are discussed. Amanita is an emblematic genus and the focus of diverse research programs. Taxonomists and users of taxonomic and systematic products are used to, and rely on, Amanita as a genus with meanin...

Ecosystem Services, 2020

Ecosystem service (ES) assessments, which make an explicit link between nature and people's well-... more Ecosystem service (ES) assessments, which make an explicit link between nature and people's well-being, can support the management of natural protected areas that face complex and persistent sustainability challenges. We present a case study of ES supply in a biosphere reserve community in southern Mexico. We aimed to identify stakeholder-relevant ES and to analyse trade-offs between them. After engaging local stakeholders, we conducted a biophysical assessment of ES supply and associations across four different land uses. Closed forests and riparian areas, which occurred in different parts of the landscape, supplied high levels of multiple ES. Furthermore, coproduced farming goods and services that supported local livelihoods and conservation-oriented ecosystem services coincided in these four habitats. Together, these habitats provided a diverse array of ES across the landscape, indicating that stakeholders benefited from a multifunctional landscape. At the same time significant trade-offs were found in the supply of forage cover against most other ES, especially tree-based goods and services. These trade-offs revealed conflicts between agricultural land and neighbouring open forests and riparian areas, as well as opposed service demands among beneficiary groups. To address these trade-offs, stakeholders agreed on enhancing forest benefits in order to support both local livelihoods and conservation goals.

Ecography, 2017

Despite the dramatic phenological responses of fungal fruiting to recent climate warming, it is u... more Despite the dramatic phenological responses of fungal fruiting to recent climate warming, it is unknown whether spatial distributions of fungi have changed and to what extent such changes are influenced by fungal traits, such as ectomycorrhizal (ECM) or saprotrophic lifestyles, spore characteristics, or fruit body size. Our overall aim was to understand how climate and fungal traits determine whether and how species-specific fungal fruit body abundances have shifted across latitudes over time, using the UK national database of fruiting records. The data employed were recorded over 45 yr (1970-2014), and include 853 278 records of Agaricales, Boletales and Russulales, though we focus only on the most common species (with more than 3000 records each). The georeferenced observations were analysed by a Bayesian inference as a Gaussian additive model with a specification following a joint species distribution model. We used an offset, random contributions and fixed effects to isolate different potential biases from the trait-specific interactions with latitude/climate and time. Our main aim was assessed by examination of the three-way-interaction of trait, predictor (latitude or climate) and time. The results show a strong trait-specific shift in latitudinal abundance through time, as ECM species have become more abundant relative to saprotrophic species in the north. Along precipitation gradients, phenology was important, in that species with shorter fruiting seasons have declined markedly in abundance in oceanic regions, whereas species with longer seasons have become relatively more common overall. These changes in fruit body distributions are correlated with temperature and rainfall, which act directly on both saprotrophic and ECM fungi, and also indirectly on ECM fungi, through altered photosynthate allocation from their hosts. If these distributional changes reflect fungal activity, there will be important consequences for the responses of forest ecosystems to changing climate, through effects on primary production and nutrient cycling.

Mycopathologia, 2006

This article appeared in a journal published by Elsevier. The attached copy is furnished to the a... more This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research and education use, including for instruction at the authors institution and sharing with colleagues. Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier's archiving and manuscript policies are encouraged to visit:

Geoderma Regional, 2015

Soil amendment with biochar has been claimed as an option for carbon (C) sequestration in agricul... more Soil amendment with biochar has been claimed as an option for carbon (C) sequestration in agricultural soils. Most studies on biochar/soil organic carbon (SOC) interactions were executed under laboratory conditions. Here we tested the stability of biochar produced in a traditional kiln and its effects on the stocks of native SOC under field conditions. The biochar was characterized using pyrolysis-gas chromatography-mass spectrometry, and then added to an Oxisol under savannah climate. This soil was amended with 0, 5, 10, 20 and 40 Mg ha −1 of biochar in a randomized complete block design with four replications and cultivated with soybean over four cropping seasons (CSs; 120 days each). Soil samples from the 0-10 cm top layer were collected at the end of the first and fourth CSs and analyzed for CO 2 emissions, isotopic C abundance (13 C/ 12 C ratio) and enzymatic activity (fluorescein diacetate and dehydrogenase). The biochar showed a low degree of thermal modification. Its relative decomposition rate was higher (k = 0.32-1.00 year −1) than generally claimed (k = 0.005-0.0005 year −1), and higher than the decomposition of native SOC (k = 0.22 year −1). Addition of biochar did not affect the stocks of native SOC. Our findings highlight the need for critically reviewing the potential of locally produced biochar to sequester C.

Epilogue: global food security, rhetoric, and the sustainable intensification debate

Current Opinion in Environmental Sustainability, 2014

ABSTRACT The need to feed nine billion people in 2050 has given rise to widespread debate in scie... more ABSTRACT The need to feed nine billion people in 2050 has given rise to widespread debate in science and policy circles. The debate is largely framed in neo-Malthusian terms, and elements of global food security (resilience of the food system, food quantity and quality, right to and access to food) demand equal attention. High-intensive agriculture, which enabled population growth and food for a large proportion of the global population, is often regarded as incompatible with current environmental (and social) sustainability. Because of the often problematic nature of high-intensive industrialized agriculture, sustainable agricultural intensification has been called an oxymoron. Pathways to sustainably intensify agriculture vary from business-as-usual to claims that a radical rethinking of our agricultural production is imperative. Three terms have been coined to differentiate such pathways. Whereas conventional intensification, that is business-as-usual, is uncontroversial (but often considered unlikely to be able to achieve environmental sustainability), the phrases sustainable intensification and ecological intensification both have a complex history. Although one could think that they have similar meanings, the phrases represent very different perspectives in discourses in science and policy circles. The terms Utopians and Arcadians are introduced for adherents of those perspectives. We observe that they both devote insufficient attention to inevitable trade-offs. Agricultural intensification in developing countries was greatly accelerated by the Green Revolution, which largely bypassed sub-Saharan Africa. Discontent with that outcome has led to a plethora of new terms to indicate more successful next steps for sub-Saharan agriculture. Industrialized agriculture as currently practised in developed countries will not provide a universal solution. This epilogue of the special issue and the literature herein show that intense debates on sustainable agricultural intensification are needed. Such debates on intensification demand reflection on the role of scientists with regard to their uses of current and the generation of novel knowledge.

Epilogue: global food security, rhetoric, and the sustainable intensification debate

Current Opinion in Environmental Sustainability, 2014

ABSTRACT The need to feed nine billion people in 2050 has given rise to widespread debate in scie... more ABSTRACT The need to feed nine billion people in 2050 has given rise to widespread debate in science and policy circles. The debate is largely framed in neo-Malthusian terms, and elements of global food security (resilience of the food system, food quantity and quality, right to and access to food) demand equal attention. High-intensive agriculture, which enabled population growth and food for a large proportion of the global population, is often regarded as incompatible with current environmental (and social) sustainability. Because of the often problematic nature of high-intensive industrialized agriculture, sustainable agricultural intensification has been called an oxymoron. Pathways to sustainably intensify agriculture vary from business-as-usual to claims that a radical rethinking of our agricultural production is imperative. Three terms have been coined to differentiate such pathways. Whereas conventional intensification, that is business-as-usual, is uncontroversial (but often considered unlikely to be able to achieve environmental sustainability), the phrases sustainable intensification and ecological intensification both have a complex history. Although one could think that they have similar meanings, the phrases represent very different perspectives in discourses in science and policy circles. The terms Utopians and Arcadians are introduced for adherents of those perspectives. We observe that they both devote insufficient attention to inevitable trade-offs. Agricultural intensification in developing countries was greatly accelerated by the Green Revolution, which largely bypassed sub-Saharan Africa. Discontent with that outcome has led to a plethora of new terms to indicate more successful next steps for sub-Saharan agriculture. Industrialized agriculture as currently practised in developed countries will not provide a universal solution. This epilogue of the special issue and the literature herein show that intense debates on sustainable agricultural intensification are needed. Such debates on intensification demand reflection on the role of scientists with regard to their uses of current and the generation of novel knowledge.

Current Opinion in Environmental Sustainability, 2014

Current Opinion in Environmental Sustainability, 2014

Assuming 'ceteris paribus' in terms of the viability of the planet during the coming half-century... more Assuming 'ceteris paribus' in terms of the viability of the planet during the coming half-century or so, the rising needs of a burgeoning, but also increasingly rich and demanding world population will drastically change agriculture. Crop yields and animal productivity will have to increase substantially, with the risk of further depleting the resource base and degrading the environment, making food production both the culprit and the victim. Future food security therefore depends on development of technologies that increase the efficiency of resource use and prevent externalization of costs. The current trend is towards intensification, especially more output per production unit so as to increase input efficiency. Whether that trend is sustainable is a matter of strong debate among scientists and policy-makers alike. The big question is how to produce more food with much fewer resources. Sustainable intensification (i.e., increasing agricultural output while keeping the ecological footprint as small as possible) for some is an oxymoron, unless real progress can be made in ecological intensification, that is, increasing agricultural output by capitalizing on ecological processes in agro-ecosystems. Definitions of intensification and sustainability vary greatly. The way these concepts are being used in different disciplines causes tensions and hides trade-offs instead of making them explicit. Inter-disciplinarity and boundary-crossing in terminology and concepts are needed. Implicitly, the operationalization of intensification and sustainability implies appreciation of and choices for values, an issue that is often overlooked and sometimes even denied in the natural sciences. The multidimensional nature of intensification needs to be linked to the various notions of sustainability, acknowledging a hierarchy of considerations underlying decision-making on trade-offs, thus allowing political and moral arguments to play a proper role in the strategy towards sustainable intensification. We make a plea to create clarity in assumptions, norms and values in that decision-making process. Acknowledging that win-win situations are rare and that (some) choices have to be made on non-scientific grounds makes the debate more transparent and its outcome more acceptable both to the scientific community and society at large.

Uien met een verbeterd wortelstelsel: vierjarig onderzoek afgerond

ABSTRACT In het kader van het onderzoeksprogramma 'Biologische productiesystemen in de ak... more ABSTRACT In het kader van het onderzoeksprogramma 'Biologische productiesystemen in de akkerbouw en vollegrondsgroenteteelt' is de afgelopen vier jaar onderzoek gedaan naar de mogelijkheden die veredeling kan bieden om het wortelstelsel van uien te verbeteren. Dit lijkt mogelijk door specifieke soortkruisingen met stengelui (Japanse bladui) en Allium roylei, met als bijkomend voordeel dat naast de selectie op een beter type wortelstelsel ook geselecteerd kan worden op resistentie tegen de bladschimmels valse meeldauw en bladvlekkenziekte. Een opvallend onderzoeksresultaat was het effect van arbusculaire mycorrhiza (AM) op het verbeteren van het wortelstelsel en de productiviteit van stengelui, en mogelijk ook ui

Mycorrhiza, 2009

Root colonization by arbuscular mycorrhizal (AM) fungi reduces stimulation of seed germination of... more Root colonization by arbuscular mycorrhizal (AM) fungi reduces stimulation of seed germination of the plant parasite Striga (Orobanchaceae). This reduction can affect not only host plants for Striga, resulting in a lower parasite incidence, but also false hosts or trap crops, which induce suicidal Striga seed germination, thereby diminishing their effectiveness. In order to better understand these AM-induced effects, we tested the influence of root colonization by different AM fungi on the seed-germination activity of root exudates of the Striga hermonthica nonhost plants cowpea and cotton on S. hermonthica. We also tested the effect of AM fungi on the seed-germination activity of the Striga gesnerioides host plant cowpea on S. gesnerioides. Moreover, we studied whether mycorrhization affects the transport of seedgermination activity to above-ground plant parts. Mycorrhization not only resulted in a lower seed germination of S. gesnerioides in the presence of root exudates of the S. gesnerioides host cowpea but also seed germination of S. hermonthica was also lower in the presence of root exudates of the S. hermonthica nonhosts cowpea and cotton. Downregulation of the Striga seedgermination activity occurs not only in root exudates upon root colonization by different AM fungi but also in the compounds produced by stems. The lowered seedgermination activity does not appear to depend on the presence of seed germination inhibitors in the root exudates of mycorrhizal plants. The implication for Striga control in the field is discussed.

Growth response of Pterocarpus soyauxii and Lophira alata seedlings to host soil mycorrhizal inoc... more Growth response of Pterocarpus soyauxii and Lophira alata seedlings to host soil mycorrhizal inocula in relation to land use types

Journal of Vegetation Science, 2016

Questions: Secondary succession in the tropics can follow alternative pathways. Land-use history ... more Questions: Secondary succession in the tropics can follow alternative pathways. Land-use history is known to engender alternative successional communities, but the underlying mechanisms driving and sustaining divergence remain unclear. In this study we aim to answer the following questions: (1) does previous land use act as a filter for species composition in secondary forests; and (2) what are the relative roles of management practices, soil properties and landscape composition in determining species composition? Location: Central Amazon, Brazil. Methods: We sampled trees, shrubs and palms (≥1cm diameter) in 38 early secondary forests (5 yr after abandonment) located along gradients of land-use intensity in five shifting cultivation landscapes. We measured the diameter and height of each sampled plant, identified it to species or morpho-species level and checked if it was resprouting or not. At each secondary forest we also collected soil samples for chemical and physical analyses and estimated the amount of old-growth forest surrounding it (landscape composition). Results: We found that previous land-use intensity determined species composition. With increasing land-use intensity, management practices of cut-andburn and associated reduction in soil quality filtered out seed-dependent species and favoured strong sprouters and species that can cope with low nutrient availability. Landscape composition had a weak effect on species assemblages. We found specific species assemblages and indicator species associated with different levels of previous land-use intensity. As a consequence of these local filters, species aand b-diversity decreased and therefore early successional communities became more similar to each other. Conclusion: Species composition of successional forests is strongly determined by different land-use intensities. Dispersal limitation has a limited effect on determining the composition of the dominant species. Filtering effects of management practices and soil quality determine the species dominating the canopy at early stages of succession and narrow down the range of species able to colonize and establish. This study highlights how land use shapes successional communities and suggests that alternative successional pathways are determined at early stages of succession. Therefore, accounting for land-use history is crucial to improve the understanding of tropical secondary succession. We present a list of indicator species for different levels of previous land-use intensity that can be used to support conservation and restoration decisions in the Amazon.

Arbuscular mycorrhizal symbiosis increases phosphorus uptake and productivity of mixtures of maize varieties compared to monocultures

Journal of Applied Ecology, 2020

Ecological intensification seeks to achieve crop yield increases by intensifying complementary or... more Ecological intensification seeks to achieve crop yield increases by intensifying complementary or facilitative interactions between plant species or varieties. Different species of arbuscular mycorrhizal fungi (AMF) exhibit niche differentiation and show selectivity towards certain plants, which can further enhance complementarity. It is not clear whether in the presence of one AMF species, where mycelial networks connect crop species, opportunities for complementarity effects may be reduced. We grew monocultures and mixtures of maize varieties in a greenhouse with one species of AMF, Funneliformis mosseae, during two consecutive years to investigate whether under such conditions the mycorrhizal symbiosis would affect complementarity and overyielding compared to non-mycorrhizal plants. Variety mixtures showed increased phosphatase activity and mycorrhizal colonization, enhanced phosphorus uptake and overyielding when plants were mycorrhizal. There was no overyielding when plants were non-mycorrhizal. The increase in relative yield total was due to complementarity effects. Synthesis and applications. Our study implies that appropriate agricultural management that enhances mycorrhizal fungal contribution to ecosystem services may result in overyielding in terms of yield or phosphorus uptake through mixing varieties within one crop species.

New Phytologist, 2021

Networks of friends and foes and the fate of tree seedlings Why are there so many different tree ... more Networks of friends and foes and the fate of tree seedlings Why are there so many different tree species in most tropical rainforests? Ecologists have increasingly turned to plant-soil feedback (PSF), the mutual interaction between plants and the soil biotic community, where plants modify, and are modified by, that soil biotic community. In the 1970s two ecologists, Daniel Janzen and Joseph Connell, independently proposed a mechanism to explain the persistence of species-rich communities through such feedbacks. The Janzen-Connell effect is based on conspecific negative density dependence (CNDD), implying larger juvenile mortality (seeds, seedlings, saplings) in the immediate vicinity of conspecific adult organisms. As a consequence of CNDD other species would be preferentially recruited under their canopy. Fungal pathogens are likely the major agent in causing seedling CNDD (Song & Corlett, 2021). Roots of tropical tree species are

ECY17-1266_SpringSapro10x10km_17jan2018

Spring saprotrophic fruiting fungi data: 10 x 10 km grid resolution of species fruiting days (ord... more Spring saprotrophic fruiting fungi data: 10 x 10 km grid resolution of species fruiting days (ordinal day; mean, 2.5 & 97.5 percentiles plus sample sizes) aggregated across 1970-2010. Associated bioclimatic meta-data for each grid are included as well. This dataset comprises saprotrophic fungal taxa fruiting in spring

Nitrogen availability mediates the priming effect of soil organic matter by preferentially altering the straw carbon-assimilating microbial community

Science of The Total Environment, 2022

Straw incorporation into soil increases carbon (C) sequestration but can induce priming effects (... more Straw incorporation into soil increases carbon (C) sequestration but can induce priming effects (PE), the enhanced breakdown of soil organic matter. The direction and magnitude of PE and the consequences for the C balance induced by straw addition depend on nitrogen (N) availability and soil management history. Using 13C-labeled maize straw, we conducted a 56-day incubation to determine the dynamics of PE and the underlying microbial mechanisms after straw and/or mineral N addition to three soils with contrasting cultivation and fertilization histories, i) unfertilized soil (Unfertilized), ii) 8 years farmyard manure amended soil (Manured), and iii) abandoned cropland soil (Abandoned). 13C-PLFAs (phospholipid fatty acids) were analyzed to identify microbial groups utilizing straw and to explore their contribution to the PE. Straw addition increased microbial biomass (MBC), activities of enzymes related to the C and N cycles, and changed microbial community composition. SOC decomposition was enhanced by microbes activated by straw addition, leading to a positive cumulative PE ranging from 494 to 789 μg C g-1 soil. The magnitude of positive PE and straw decomposition in the manured soil was higher than that in the unfertilized and abandoned soils due to larger MBC and higher enzyme activities, resulting in a lower net SOC gain. Compared with straw only, the combination of straw addition with N fertilizer did not influence MBC, but increased positive PE (average increase of 18.1%) and straw decomposition (17.1%), further limiting SOC gain. 13C-labeled fungi: bacteria ratios and Gram-positive (G+): negative (G-) bacteria ratios increased with the increasing PE after N fertilization, but soil-derived (un-labeled) PLFAs remained stable. Random forest analysis further showed that straw C-assimilating microbial attributes are important predictors in driving the greater PE after N addition. Our study highlights the importance of straw C-assimilating fungi and G+ bacteria in mediating N-induced PE in arable soils.

Conventional wisdom considers the mycorrhizal symbiosis as mutualistic because both the mycorrhiz... more Conventional wisdom considers the mycorrhizal symbiosis as mutualistic because both the mycorrhizal fungus and the mycorrhizal plant potentially benefit from the exchange of nutrients and carbon (C). Cases in which mycorrhizal plants are smaller than nonmycorrhizal plants have been reported (Klironomos, 2003). While these cases are often considered exceptions, they raise an important question of partner control. How do plant and fungal partners ensure that they are getting a ‘fair-deal’ for the resources they are trading, and avoid being cheated (Ghoul et al., 2014)? Does engaging in amutualistic partnership translate into consistent andmeasurable benefits? Recently, N€asholm et al. (2013) explicitly addressed the question of whether ectomycorrhizal fungi alleviate or aggravate nitrogen (N) limitation of conifers in boreal forests. They concluded that, in these systems, ectomycorrhizal fungi immobilize large quantities of N and thus drive N limitation for host plants. In this issue ...

During the last few years a large number of new mushroom genera have been described. In many case... more During the last few years a large number of new mushroom genera have been described. In many cases such new genera were proposed as a consequence of molecular phylogenetic research, whereas morphological support for these genera was in a number of cases not presented. In this paper we discuss a number of these changes (boletes, the previous genus Clitocybe; in both cases a large number of new genera were proposed). We also ask the question to what extent such changes have to be followed. At the end we introduce a number of criteria that are helpful in judging whether such new genera are indeed indicative of taxonomical progress. It is clear that many of the new genera do not (yet) fulfil these criteria

Recently the well-known genus Amanita has been split into two genera, Amanita, a genus of putativ... more Recently the well-known genus Amanita has been split into two genera, Amanita, a genus of putatively ectomycorrhizal fungi, and Saproamanita, a genus of putatively saprotrophic fungi. We disagree with this generic split and argue why Amanita should not be split. The proposal to split the genus does not conform to the recently proposed guidelines for publishing new genera. Concise amended characterizations are provided for the monophyletic family Amanitaceae and its two monophyletic genera Amanita and Limacella.2 The characterization of Amanita rests on a single, unique synapomorphy—schizohymenial ontogeny in its agaricoid and secotioid taxa. We propose a minimal reorganization of Amanita—removal of stirps Hesleri from subsection Vittadiniae. Some open issues in Amanita systematics are discussed. Amanita is an emblematic genus and the focus of diverse research programs. Taxonomists and users of taxonomic and systematic products are used to, and rely on, Amanita as a genus with meanin...

Ecosystem Services, 2020

Ecosystem service (ES) assessments, which make an explicit link between nature and people's well-... more Ecosystem service (ES) assessments, which make an explicit link between nature and people's well-being, can support the management of natural protected areas that face complex and persistent sustainability challenges. We present a case study of ES supply in a biosphere reserve community in southern Mexico. We aimed to identify stakeholder-relevant ES and to analyse trade-offs between them. After engaging local stakeholders, we conducted a biophysical assessment of ES supply and associations across four different land uses. Closed forests and riparian areas, which occurred in different parts of the landscape, supplied high levels of multiple ES. Furthermore, coproduced farming goods and services that supported local livelihoods and conservation-oriented ecosystem services coincided in these four habitats. Together, these habitats provided a diverse array of ES across the landscape, indicating that stakeholders benefited from a multifunctional landscape. At the same time significant trade-offs were found in the supply of forage cover against most other ES, especially tree-based goods and services. These trade-offs revealed conflicts between agricultural land and neighbouring open forests and riparian areas, as well as opposed service demands among beneficiary groups. To address these trade-offs, stakeholders agreed on enhancing forest benefits in order to support both local livelihoods and conservation goals.

Ecography, 2017

Despite the dramatic phenological responses of fungal fruiting to recent climate warming, it is u... more Despite the dramatic phenological responses of fungal fruiting to recent climate warming, it is unknown whether spatial distributions of fungi have changed and to what extent such changes are influenced by fungal traits, such as ectomycorrhizal (ECM) or saprotrophic lifestyles, spore characteristics, or fruit body size. Our overall aim was to understand how climate and fungal traits determine whether and how species-specific fungal fruit body abundances have shifted across latitudes over time, using the UK national database of fruiting records. The data employed were recorded over 45 yr (1970-2014), and include 853 278 records of Agaricales, Boletales and Russulales, though we focus only on the most common species (with more than 3000 records each). The georeferenced observations were analysed by a Bayesian inference as a Gaussian additive model with a specification following a joint species distribution model. We used an offset, random contributions and fixed effects to isolate different potential biases from the trait-specific interactions with latitude/climate and time. Our main aim was assessed by examination of the three-way-interaction of trait, predictor (latitude or climate) and time. The results show a strong trait-specific shift in latitudinal abundance through time, as ECM species have become more abundant relative to saprotrophic species in the north. Along precipitation gradients, phenology was important, in that species with shorter fruiting seasons have declined markedly in abundance in oceanic regions, whereas species with longer seasons have become relatively more common overall. These changes in fruit body distributions are correlated with temperature and rainfall, which act directly on both saprotrophic and ECM fungi, and also indirectly on ECM fungi, through altered photosynthate allocation from their hosts. If these distributional changes reflect fungal activity, there will be important consequences for the responses of forest ecosystems to changing climate, through effects on primary production and nutrient cycling.

Mycopathologia, 2006

This article appeared in a journal published by Elsevier. The attached copy is furnished to the a... more This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research and education use, including for instruction at the authors institution and sharing with colleagues. Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier's archiving and manuscript policies are encouraged to visit:

Geoderma Regional, 2015

Soil amendment with biochar has been claimed as an option for carbon (C) sequestration in agricul... more Soil amendment with biochar has been claimed as an option for carbon (C) sequestration in agricultural soils. Most studies on biochar/soil organic carbon (SOC) interactions were executed under laboratory conditions. Here we tested the stability of biochar produced in a traditional kiln and its effects on the stocks of native SOC under field conditions. The biochar was characterized using pyrolysis-gas chromatography-mass spectrometry, and then added to an Oxisol under savannah climate. This soil was amended with 0, 5, 10, 20 and 40 Mg ha −1 of biochar in a randomized complete block design with four replications and cultivated with soybean over four cropping seasons (CSs; 120 days each). Soil samples from the 0-10 cm top layer were collected at the end of the first and fourth CSs and analyzed for CO 2 emissions, isotopic C abundance (13 C/ 12 C ratio) and enzymatic activity (fluorescein diacetate and dehydrogenase). The biochar showed a low degree of thermal modification. Its relative decomposition rate was higher (k = 0.32-1.00 year −1) than generally claimed (k = 0.005-0.0005 year −1), and higher than the decomposition of native SOC (k = 0.22 year −1). Addition of biochar did not affect the stocks of native SOC. Our findings highlight the need for critically reviewing the potential of locally produced biochar to sequester C.

Epilogue: global food security, rhetoric, and the sustainable intensification debate

Current Opinion in Environmental Sustainability, 2014

ABSTRACT The need to feed nine billion people in 2050 has given rise to widespread debate in scie... more ABSTRACT The need to feed nine billion people in 2050 has given rise to widespread debate in science and policy circles. The debate is largely framed in neo-Malthusian terms, and elements of global food security (resilience of the food system, food quantity and quality, right to and access to food) demand equal attention. High-intensive agriculture, which enabled population growth and food for a large proportion of the global population, is often regarded as incompatible with current environmental (and social) sustainability. Because of the often problematic nature of high-intensive industrialized agriculture, sustainable agricultural intensification has been called an oxymoron. Pathways to sustainably intensify agriculture vary from business-as-usual to claims that a radical rethinking of our agricultural production is imperative. Three terms have been coined to differentiate such pathways. Whereas conventional intensification, that is business-as-usual, is uncontroversial (but often considered unlikely to be able to achieve environmental sustainability), the phrases sustainable intensification and ecological intensification both have a complex history. Although one could think that they have similar meanings, the phrases represent very different perspectives in discourses in science and policy circles. The terms Utopians and Arcadians are introduced for adherents of those perspectives. We observe that they both devote insufficient attention to inevitable trade-offs. Agricultural intensification in developing countries was greatly accelerated by the Green Revolution, which largely bypassed sub-Saharan Africa. Discontent with that outcome has led to a plethora of new terms to indicate more successful next steps for sub-Saharan agriculture. Industrialized agriculture as currently practised in developed countries will not provide a universal solution. This epilogue of the special issue and the literature herein show that intense debates on sustainable agricultural intensification are needed. Such debates on intensification demand reflection on the role of scientists with regard to their uses of current and the generation of novel knowledge.

Epilogue: global food security, rhetoric, and the sustainable intensification debate

Current Opinion in Environmental Sustainability, 2014

ABSTRACT The need to feed nine billion people in 2050 has given rise to widespread debate in scie... more ABSTRACT The need to feed nine billion people in 2050 has given rise to widespread debate in science and policy circles. The debate is largely framed in neo-Malthusian terms, and elements of global food security (resilience of the food system, food quantity and quality, right to and access to food) demand equal attention. High-intensive agriculture, which enabled population growth and food for a large proportion of the global population, is often regarded as incompatible with current environmental (and social) sustainability. Because of the often problematic nature of high-intensive industrialized agriculture, sustainable agricultural intensification has been called an oxymoron. Pathways to sustainably intensify agriculture vary from business-as-usual to claims that a radical rethinking of our agricultural production is imperative. Three terms have been coined to differentiate such pathways. Whereas conventional intensification, that is business-as-usual, is uncontroversial (but often considered unlikely to be able to achieve environmental sustainability), the phrases sustainable intensification and ecological intensification both have a complex history. Although one could think that they have similar meanings, the phrases represent very different perspectives in discourses in science and policy circles. The terms Utopians and Arcadians are introduced for adherents of those perspectives. We observe that they both devote insufficient attention to inevitable trade-offs. Agricultural intensification in developing countries was greatly accelerated by the Green Revolution, which largely bypassed sub-Saharan Africa. Discontent with that outcome has led to a plethora of new terms to indicate more successful next steps for sub-Saharan agriculture. Industrialized agriculture as currently practised in developed countries will not provide a universal solution. This epilogue of the special issue and the literature herein show that intense debates on sustainable agricultural intensification are needed. Such debates on intensification demand reflection on the role of scientists with regard to their uses of current and the generation of novel knowledge.

Current Opinion in Environmental Sustainability, 2014

Current Opinion in Environmental Sustainability, 2014

Assuming 'ceteris paribus' in terms of the viability of the planet during the coming half-century... more Assuming 'ceteris paribus' in terms of the viability of the planet during the coming half-century or so, the rising needs of a burgeoning, but also increasingly rich and demanding world population will drastically change agriculture. Crop yields and animal productivity will have to increase substantially, with the risk of further depleting the resource base and degrading the environment, making food production both the culprit and the victim. Future food security therefore depends on development of technologies that increase the efficiency of resource use and prevent externalization of costs. The current trend is towards intensification, especially more output per production unit so as to increase input efficiency. Whether that trend is sustainable is a matter of strong debate among scientists and policy-makers alike. The big question is how to produce more food with much fewer resources. Sustainable intensification (i.e., increasing agricultural output while keeping the ecological footprint as small as possible) for some is an oxymoron, unless real progress can be made in ecological intensification, that is, increasing agricultural output by capitalizing on ecological processes in agro-ecosystems. Definitions of intensification and sustainability vary greatly. The way these concepts are being used in different disciplines causes tensions and hides trade-offs instead of making them explicit. Inter-disciplinarity and boundary-crossing in terminology and concepts are needed. Implicitly, the operationalization of intensification and sustainability implies appreciation of and choices for values, an issue that is often overlooked and sometimes even denied in the natural sciences. The multidimensional nature of intensification needs to be linked to the various notions of sustainability, acknowledging a hierarchy of considerations underlying decision-making on trade-offs, thus allowing political and moral arguments to play a proper role in the strategy towards sustainable intensification. We make a plea to create clarity in assumptions, norms and values in that decision-making process. Acknowledging that win-win situations are rare and that (some) choices have to be made on non-scientific grounds makes the debate more transparent and its outcome more acceptable both to the scientific community and society at large.

Uien met een verbeterd wortelstelsel: vierjarig onderzoek afgerond

ABSTRACT In het kader van het onderzoeksprogramma 'Biologische productiesystemen in de ak... more ABSTRACT In het kader van het onderzoeksprogramma 'Biologische productiesystemen in de akkerbouw en vollegrondsgroenteteelt' is de afgelopen vier jaar onderzoek gedaan naar de mogelijkheden die veredeling kan bieden om het wortelstelsel van uien te verbeteren. Dit lijkt mogelijk door specifieke soortkruisingen met stengelui (Japanse bladui) en Allium roylei, met als bijkomend voordeel dat naast de selectie op een beter type wortelstelsel ook geselecteerd kan worden op resistentie tegen de bladschimmels valse meeldauw en bladvlekkenziekte. Een opvallend onderzoeksresultaat was het effect van arbusculaire mycorrhiza (AM) op het verbeteren van het wortelstelsel en de productiviteit van stengelui, en mogelijk ook ui

Mycorrhiza, 2009

Root colonization by arbuscular mycorrhizal (AM) fungi reduces stimulation of seed germination of... more Root colonization by arbuscular mycorrhizal (AM) fungi reduces stimulation of seed germination of the plant parasite Striga (Orobanchaceae). This reduction can affect not only host plants for Striga, resulting in a lower parasite incidence, but also false hosts or trap crops, which induce suicidal Striga seed germination, thereby diminishing their effectiveness. In order to better understand these AM-induced effects, we tested the influence of root colonization by different AM fungi on the seed-germination activity of root exudates of the Striga hermonthica nonhost plants cowpea and cotton on S. hermonthica. We also tested the effect of AM fungi on the seed-germination activity of the Striga gesnerioides host plant cowpea on S. gesnerioides. Moreover, we studied whether mycorrhization affects the transport of seedgermination activity to above-ground plant parts. Mycorrhization not only resulted in a lower seed germination of S. gesnerioides in the presence of root exudates of the S. gesnerioides host cowpea but also seed germination of S. hermonthica was also lower in the presence of root exudates of the S. hermonthica nonhosts cowpea and cotton. Downregulation of the Striga seedgermination activity occurs not only in root exudates upon root colonization by different AM fungi but also in the compounds produced by stems. The lowered seedgermination activity does not appear to depend on the presence of seed germination inhibitors in the root exudates of mycorrhizal plants. The implication for Striga control in the field is discussed.